## Warning: package 'ggplot2' was built under R version 3.6.3
## Warning: package 'igraph' was built under R version 3.6.3
## Warning: package 'markovchain' was built under R version 3.6.3
## Warning: package 'gridExtra' was built under R version 3.6.3
## [1] 5.9840548 3.7404996 2.0896780 1.3230250 1.1019674 0.9766566 0.9021602
## [8] 0.6464166 0.5868130 0.5087633 0.4418356 0.3914422 0.3474311 0.3149250
## [15] 0.3031454 0.2890737 0.2568495 0.2294809 0.2250794 0.2010400
## [1] -0.05442782 -0.06150271 -0.07856958 -0.09270186 -0.10894815 -0.12931259
We will use the gap statistic to indicate the number of clusters in this data:
Perform PAM 3-fold clusters:
##### ................... ###Heatmap
##### Boxplots for each genus in the three clusters
#### adjusted pvalues for kruskal tests By Benjamini-Hochberg
| adjusted_pvalue |
|---|
| 0.0000246 |
| 0.0000246 |
| 0.0092642 |
| 0.0092642 |
| 0.0092642 |
| 0.0096930 |
| 0.0119068 |
| 0.0122253 |
| 0.0157795 |
| 0.0190393 |
| 0.0220737 |
| 0.0220737 |
| 0.0220737 |
| 0.0220737 |
| 0.0266533 |
| 0.0272881 |
| 0.0283403 |
| 0.0335325 |
| 0.0335325 |
| 0.0335325 |
| 0.0361313 |
| 0.0382899 |
| 0.0444898 |
| 0.0444898 |
| 0.0444898 |
| 0.0444898 |
| 0.0444898 |
| 0.0444898 |
| 0.0444898 |
| 0.0444898 |
| 0.0444898 |
| 0.0444898 |
| 0.0444898 |
| 0.0444898 |
| 0.0444898 |
| 0.0444898 |
| 0.0451622 |
| 0.0451622 |
| Veg | Mixed | |
|---|---|---|
| Clust.1 | 53.3 | 46.7 |
## Diet
## CST Mixed Veg Sum
## 1 14 16 30
## 2 5 8 13
## 3 9 6 15
## Sum 28 30 58
## [1] "Fisher exact test p-value is: "
## [1] 0.5411113